Schaffner had been collecting Beatles memorabilia through much of the 1960s, which directly led to his first book, The Beatles Forever, published in 1977. With its critical acceptance, he was established as an authority on the Beatles. Among initial reviews of the book, The New York Post described it as “honest, factual and highly entertaining”, while Publishers Weekly said: “May well be the book for Beatlemaniacs … All-inclusive, responsible and informative …” Schaffner subsequently appeared as a commentator in a 1982 documentary about the group, titled The Complete Beatles.

The Beatles Forever continues to be held in high regard by writers and commentators. While discussing the most recent generation of Beatles biographies in December 2013, Chicago Tribune critic Mark Caro recalled its publication and described the book as “the superior critical-minded history” on the band. Ian Inglis, author of a 2010 biography on George Harrison, wrote of Schaffner’s contribution: “Among the very best of the hundreds of books that examine the history of the Beatles. Intelligently written …”

As an author, his other works include the Pink Floyd biography A Saucerful of Secrets: The Pink Floyd Odyssey as well as the children’s book The Boys from Liverpool: John, Paul, George, Ringo. In 1981 he collaborated with his sister, Elizabeth, on 505 Rock-and-Roll Questions Your Friends Can’t Answer. Schaffner also wrote articles for Rolling Stone, Musician, The Village Voice, and Trouser Press.

Schaffner died on August 28, 1991 in New York City of an AIDS-related illness shortly after the release of Saucerful of Secrets: The Pink Floyd Odyssey.

Schaffner’s song cycle, Magical Kingdoms, was released in 1990. Music from the collection has been performed posthumously at tribute events at venues including New York’s Lincoln Center.